huerqiang commented 1 year ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/YuLab-SMU/GeoTcgaData

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bioc-issue-bot commented 1 year ago

Hi @huerqiang

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: GeoTcgaData
Type: Package
Title: Processing Various Types of Data on GEO and TCGA
Version: 0.99.0
Authors@R: person(given = "Erqiang", family = "Hu", email = "13766876214@163.com", role  = c("aut", "cre"), comment = c(ORCID = "0000-0002-1798-7513"))
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) 
    provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP
    and Copy number variation data. It's easy to download data from TCGA using the 
    gdc tool, but processing these data into a format suitable for bioinformatics 
    analysis requires more work. This R package was developed to handle these data.
Depends: R (>= 4.2.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.1
Suggests: 
    knitr,
    rmarkdown,
    DESeq2,
    S4Vectors,
    ChAMP,
    impute,
    tidyr,
    clusterProfiler,
    org.Hs.eg.db,
    edgeR,
    limma,
    quantreg,
    minfi,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    dearseq,
    NOISeq,
    testthat (>= 3.0.0),
    CATT,
    TCGAbiolinks,
    enrichplot
VignetteBuilder: knitr
Imports: 
    utils,
    data.table,
    magrittr,
    plyr,
    cqn,
    dplyr,
    topconfects,
    stats
Language: en-US
URL: https://github.com/YuLab-SMU/GeoTcgaData
BugReports: https://github.com/YuLab-SMU/GeoTcgaData/issues
biocViews: GeneExpression, DifferentialExpression, RNASeq, 
    CopyNumberVariation, Microarray, Software, DNAMethylation,
    DifferentialMethylation, SNP, ATACSeq
Config/testthat/edition: 3

bioc-issue-bot commented 1 year ago

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bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

huerqiang commented 1 year ago

@LiNk-NY Hi, I see there is an errror: 'ERROR: System files found that should not be Git tracked. GeoTcgaData.Rproj'. I have delete this rproj file. And there is also a warning: 'directory GeoTcgaData/man/figures is empty'. I don't know what's causing this. The GeoTcgaData/man/figures folder isn't empty. Can you help me with this warning? Thank you very much.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6fdec848adc14d51cfc5b1e4aa3f9a841d8febae

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 1 year ago

Hi ErQiang, @huerqiang

Thank you for your submission. Please see below.

Best regards, Marcel

GeoTcgaData #2862

After a cursory review, it seems that the package does not integrate well with Bioconductor. It uses data.frame as the common output formats, it does not depend on any Bioconductor packages, e.g., SummarizedExperiment, and it does not follow Bioconductor Package Guidelines https://contributions.bioconductor.org/. Suggesting Bioconductor packages is not enough to merit Bioconductor inclusion. If you would like the package to be reconsidered, please make use of common Bioconductor classes seen at https://contributions.bioconductor.org/important-bioconductor-package-development-features.html#reusebioc

DESCRIPTION

Remove LazyData field
Looks good.

NAMESPACE

Use the native pipe |> instead of magrittr's %>%.
Consider avoiding the vague term "diff" in function names.
Avoid vague names e.g., rep1 and rep2
Avoid class names in functions e.g., *_matrix, *_vector instead make clear the return value in the documentation.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3597915f23de7ae1dd982e25a09c41a4ee03daa4

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 92c2306163eb75b7a271def8eac4799a7da0d4ab

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

huerqiang commented 1 year ago

@LiNk-NY Hi, we have updated the package, and now it can use SummarizedExperiment object. We have also changed functions, such as rep1, rep2, matrix, and diff.

LiNk-NY commented 1 year ago

Hi ErQiang, @huerqiang

Thank you for making those changes. Please see the review below.

Best, Marcel

GeoTcgaData #2862

Update the version so that it is greater than the last known version on CRAN (1.1.1)

DESCRIPTION

Looks good.

NAMESPACE

Avoid long function names like differential_RNA_SummarizedExperiment and methydifferential_SummarizedExperiment. The name of the compatible class does not need to be in the function name.
Avoid using sink and use standard functions to suppress messages, e.g., suppressMessages etc., if necessary.

/

Remove the docs folder from the package. It gets populated when the package is built.
Include only one .gitignore in the base folder
Remove cran-comments.md

vignettes

Avoid using eval=FALSE in the vignettes. Any package submitted to Bioconductor should have a runnable vignette.

R

Provide a proper description and full documentation of arguments for all functions, including arrayDiff.
Describe in detail, where the data come from in R/data.R. If possible, use more descriptive names.
Merge_methy_tcga should take data.frames as inputs rather than files. If files are absolutely necessary, include a precise description of the files and the directory structure. You could also provide a helper function to read in the methylation files from a directory which could then serve as the input to the merge operation.
Avoid the using sink and remove the quiet function. Use utils::capture.output, if needed.
Create a single methydifferential / differential_RNA function that handles matrix, data.frame, and SummarizedExperiment inputs.
Avoid functions that work with directory inputs. Interoperable functions should operate on the base data representations i.e., DataFrame, matrix, etc. (see tcga_cli_deal)
Remove commented code.
See our Data section at https://contributions.bioconductor.org/data.html?q=Data#exported-data-and-the-data-directory for id_conversion
Make sure datasets in the package have proper type conversion. That is columns like entrez_id, gene_len, start, end etc. are numeric.

tests

Include more tests for your functions.

> covr::package_coverage()
GeoTcgaData Coverage: 2.25%
R/calculate_mean_module.R: 0.00%
R/calculate_mean_profile.R: 0.00%
R/CNV.R: 0.00%
R/fpkm_count_conversion.r: 0.00%
R/id_conversion_all.r: 0.00%
R/prepareChi.r: 0.00%
R/Proce_cli.R: 0.00%
R/rep.R: 0.00%
R/RNA_seq.R: 0.00%
R/SNP.R: 0.00%
R/TCGA_id_conversion.R: 0.00%
R/utilities.R: 0.00%
R/Merge_methylation.R: 8.07%
R/arrayDiff.R: 22.22%

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: df33e57fbf0a718b213dbd78a87a1d7a0a285e35

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c82c7deea2338cf7857b6b04e0828128e37d6bb3

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

huerqiang commented 1 year ago

@LiNk-NY Hi, I have fixed these issues: (1) Update the version so that it is greater than the last known version on CRAN (1.1.1) When I update it to 1.1.2, I get the error whe push: remote: Error: Illegal version bump from '0.99.3' to '1.1.2'. So I changed it to '0.99.5' (2)Avoid long function names like differential_RNA_SummarizedExperiment and methydifferential_SummarizedExperiment. The name of the compatible class does not need to be in the function name. I changed to use generic functions for differential_RNA and differential_methy (3)Avoid using sink and use standard functions to suppress messages, e.g., suppressMessages etc., if necessary. I removed the quiet function who use sink. (4)Include only one .gitignore in the base folder. I removed other files in the base folder. (5)Provide a proper description and full documentation of arguments for all functions, including arrayDiff. Describe in detail, where the data come from in R/data.R. If possible, use more descriptive names I have updated the documents of the functions and data. (6)Merge_methy_tcga should take data.frames as inputs rather than files. If files are absolutely necessary, include a precise description of the files and the directory structure. You could also provide a helper function to read in the methylation files from a directory which could then serve as the input to the merge operation. The function Merge_methy_tcga() is used to merge methylation data downloaded from TCGA. When the methylation data is downloaded from TCGA, each sample is saved in a folder, which contains the methylation value file and the descriptive file. So the input need to be a directory. And I have update the document of this function. (7)Avoid the using sink and remove the quiet function. Use utils::capture.output, if needed. I removed the quiet function. (8)Create a single methydifferential / differential_RNA function that handles matrix, data.frame, and SummarizedExperiment inputs. I changed to use generic functions for differential_RNA and differential_methy (9)Avoid functions that work with directory inputs. Interoperable functions should operate on the base data representations i.e., DataFrame, matrix, etc. (see tcga_cli_deal) I removed the tcga_cli_deal function. (10)Remove commented code I removed the commented code. (11)See our Data section at https://contributions.bioconductor.org/data.html?q=Data#exported-data-and-the-data-directory for id_conversion This id_conversion function doesn't need to be used, so I removed it. (12)Make sure datasets in the package have proper type conversion. That is columns like entrez_id, gene_len, start, end etc. are numeric. I am sure they are correct. (13)Include more tests for your functions.

covr::package_coverage() GeoTcgaData Coverage: 24.29% R/AllGenerics.R: 0.00% R/RNA_seq.R: 0.00% R/SNP.R: 0.00% R/TCGA_id_conversion.R: 0.00% R/arrayDiff.R: 4.60% R/Merge_methylation.R: 26.58% R/CNV.R: 82.76% R/fpkm_count_conversion.r: 89.58% R/calculate_mean_module.R: 100.00% R/calculate_mean_profile.R: 100.00% R/prepareChi.r: 100.00% R/rep.R: 100.00%

LiNk-NY commented 1 year ago

Hi Erqiang, @huerqiang

Thank you for making those changes. The documentation looks better. There are still a few unresolved comments with the package.

When I update it to 1.1.2, I get the error whe push: remote: Error: Illegal version bump from '0.99.3' to '1.1.2'. So I changed it to '0.99.5'

Please keep it at a version number above the CRAN release, e.g., 1.99.0. We will update accordingly to accept the version. cc: @lshep

Avoid creating S3 / S4 methods for classes you do not own. differential_methy should be a plain function that can handle matrix, SummarizedExperiment, and other data structures.
Remove functions e.g., differential_methy.matrix etc. create a plain function as above.

Best, Marcel

huerqiang commented 1 year ago

@LiNk-NY Hi, I have update the version to '1.99.0' and use the plain functions 'differential_methy' and 'differential_RNA' instead of generic functions.

lshep commented 1 year ago

@huerqiang I have temporarily made an exception to the hook and you should be able to push the updated version to git.bioconductor.org. Please proceed and let me know when you are finished so we can re-establish the hook when you are done to prevent any bad version numbers. To Confirm: it should be 1.99.0 and then any further changes simply bump the z of version x.y.z . Cheers

huerqiang commented 1 year ago

@lshep Hi， I have push to the BioC and it now shows:

$ git push upstream master
Everything up-to-date

The version now is '1.99.0'.

lshep commented 1 year ago

Can you please check again and that you have the remotes set up correctly? When I pulled from git@git.bioconductor.org:packages/GeoTcgaData it is still showing 0.99.5

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 18b9e186b8c3bd60dd5173f34d0612d8f8c3d08c

lshep commented 1 year ago

thank you!

huerqiang commented 1 year ago

@lshep I push it again, and it should be OK now. I don't know why it failed before.

lshep commented 1 year ago

yes I can see it now. thank you. You'll likely get a note in the BiocCheck about have 1.99.0 which can be ignored in this case.

LiNk-NY commented 1 year ago

Thanks Lori! @lshep

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/GeoTcgaData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

huerqiang commented 1 year ago

@LiNk-NY @lshep Hi, do I need to make any other changes?

huerqiang commented 1 year ago

@LiNk-NY @lshep Hi, since April 19 is the deadline to add new packages to the Bioc 3.17 manifest, so can we speed up the review process? Is there anything I need to change?

LiNk-NY commented 1 year ago

Hi ErQiang, @huerqiang Sorry for the delay. It looks like the package is good to go. Thank you for your submission. Best regards, Marcel

bioc-issue-bot commented 1 year ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

lshep commented 1 year ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/huerqiang.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("GeoTcgaData"). The package 'landing page' will be created at

https://bioconductor.org/packages/GeoTcgaData

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

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